The organization of biochemical networks that make up the living cell can be defined by studying the dynamics of protein-protein interactions. To this end, experimental strategies based on protein fragment complementation assays (PCAs) have been used to map biochemical networks and to identify novel components of these networks. Pharmacological perturbations of the interactions can be observed, and the resulting pharmacological profiles and subcellular locations of interactions allow each gene product to be 'placed' at its relevant point in a network. Network mapping by PCA could be used with, or instead of, traditional target-based drug discovery strategies to increase the quantity and quality of information about the actions of small molecules on living cells and the intricate networks that make up their chemical machinery.